[Academic tech] Hardware I use – Simulations, photogrammetry, and dissection

In a similar vein to my ‘Software I use’ post, I want to run through what I’m using in terms of hardware in day-to-day use, both directly for research and for general lecturing/computer-y things.

Most of what I do these days takes place on the computer, whether that’s simulating dinosaur footprints, or writing/giving lectures, so let’s start there…

Computers:

Personal (desktop)

My personal home computer is the same machine I’ve been running all of my photogrammetry testing scenarios on for the blog, because while it’s decent enough, it’s nothing special or outrageously expensive. Let’s be upfront about this, it was bought for the dual purposes of science and computer games. It’s a few years old now (bought 2015), but still runs everything I need it to at a decent speed. The specs are as follows:

• Intel i7 – 4790k
• 4 GB Nvidia GTX 970
• 16 GB RAM
• Water cooling (I like my PCs to be silent, but probably wouldn’t go this route again, as it makes taking everything apart so much more difficult).
• 256gb SSD + 1TB HDD
• And that’s all wrapped up in a lovely micro ATX case for compactness.

I ordered the computer from dinopc.com – obviously the name of the company was an attraction, but this is actually the second PC I’ve bought from them, I was so impressed by the first. All the cables and internals are expertly and neatly arranged, the price was great, and the customizability meant I could get exactly what I wanted. Unless Microsoft bring out an upgradable surface studio in the next couple of years, my next PC will be from DinoPC too!

That machine is hooked up to an Asus MX27AQ monitor, which is a decent size and resolution (27”, 1440p) and has a good built in speaker. You can see that on amazon here: https://amzn.to/2J0rWzT.

Personal (mobile)

Until just last week, I’d been carrying around an i5 Surface Pro 3 from Microsoft. Without a doubt, this machine has been fantastic. In and of itself, it was powerful enough to run Maya, Meshlab, Adobe Photoshop/Illustrator, which meant I could use it to edit talks/papers on the go, render out animations before a talk if I needed to, and process images from my high speed camera (see below) in the field. Awesome. At work, I used it for every lecture, hooking it up to whatever connection was available with a handy HDMI/VGA/DVI adaptor, and using the button on the pen to change slides, and the pen itself to draw on the slides when a whiteboard wasn’t available. It was awesome and I can’t recommend the surface line enough. You can get the new 6^th generation either from Microsoft or from a cheeky Amazon Affiliate link like this one: https://amzn.to/2yKITd7. They start at the best part of £900 (without keyboard), but in my opinion that’s totally worth it for a laptop/tablet that can do as much as they can. Alternatively, a Surface Pro 3 like mine can be had refurbished for under £400, though obviously the internals are starting to get a bit dated.

Unfortunately, on my way back from a lecture last week I dropped it right on the corner and the screen cracked. I’d been eyeing up the new Surface Go for a while, so I’ll be replacing my Surface Pro with that in the near future, and possibly putting up a review.

Work (office)

My office computer is a Dell Precision M3800, hooked up to a 27”1440p monitor. I was lucky enough to convince my institution to get me this when I started at LJMU, and it’s been a real workhorse for the past 3 and a half years.

For the record, the specs are:

• Intel i7-4712HQ (2.30 GHz)
• Intel HD4600 and 2 GB Nvidia Quadro K1100M
• 16 GB RAM
• 512 GB SSD

However, it’s really starting to show its age, and now lives with a fan perpetually aimed at the base so it can maintain top processor speeds. It originally came with windows 8 (which I was a big fan of), but when I upgraded to Win 10 it never quite felt snappy. The problem is the display is 4k, and while the Quadro is powerful enough for photogrammetry, rendering etc, the display itself is powered by the intel HD4600 which can’t run 4k smoothly to save it’s life, so using the start menu or task-switcher in windows has just the hint of lag, which drives me up the wall. As such, I recently took to hooking it up to the 1440p monitor and disabling the laptop screen. Makes things much snappier.

I really need an upgrade, but unfortunately, I’ll need to budget that into a grant, as my institution won’t provide anything but the barest of bones boxes (at outrageous prices, due to rules requiring them to only use one provider). On top of that, IT services at LJMU now have the policy that no-one is allowed admin rights temporary or otherwise, so we can’t install any software unless requested and deployed through central IT. That does not a good workflow make, especially for someone who spends a lot of research time finding the best software and methods. So, I’m not sure what I’ll do here, going forwards.

Work (lab)

Up in the lab, we’ve got a large Dell Precision T9710 workstation. This is where I run most of my simulations and large-scale photogrammetry reconstructions. The whole lab has access to this machine, and it’s often running something of mine in the background while someone else is logged in, and handles everything pretty well. The biggest thing is the number of processors – I can run mpi software like LIGGGHTS on 48 processors, which let’s me run all but my largest simulations (albeit over a week, rather than a day on the supercomputer). It also has a pretty beefy Quadro card which is great for photogrammetry and rendering. My only reservation here is that in the future I’d always go with consumer GeForce cards instead – you get way more ‘bang for your buck’, and most software I’m using is optimized for consumer, rather than (or as well as) scientific, GPUs.

It’s hooked up to a 4k display, and has the following specs:

• Two Intel Xeon E5-2670 CPUs (2.60 GHz), each with 12 cores (with hyperthreading, that gives me total 24 cores/48 processors)
• 8 GB Nvidia Quadro K5200
• 64 GB Ram
• 2x 256 GB SSD (I know…. These are way too small and I need a larger HDD).

The workstation is as old as the laptop, and the internals certainly aren’t the fastest out there, but it’s the largest computer I have access to and will see me through for another couple of years I imagine.

Camera equipment:

My camera is an important part of my equipment, both for photogrammetry and recording motion (which gets used in lectures, research, and put on my youtube channel)

Main camera

My main camera is a Sony Nex-6, for which I have three lenses: 35 mm prime, 16-50mm compact, and 55-210 telephoto. I’ve had this camera for 6 years now, and haven’t once felt the need to replace it.

Back in 2006-2008 I had an Olympus e-500, which was massive, and while it took nice photos, I just never took it with me when I went out and about. I replaced that with a Cannon G10, which was superb and got used to death, but had a small sensor and limited flexibility from its fixed lens. The Nex-6 is the perfect balance: with the 16-50mm lens I can put the whole thing in my coat pocket. If I know I’m going out specifically to take photos, I can pack the appropriate lenses.

On the one hand, I’d love to go to full-frame, rather than the APS-C sensor in the Nex-6, to try and squeeze a bit more detail out, and especially to deal with low-light better (museums tend to be on the dark side). But no full-frame camera, including Sony’s A7 series, is as small and portable. The A7’s, which are the natural upgrade path, have a view-finder on top which just makes the camera un-pocketable, while the A-6000 series are slightly chunkier without offering me enough benefits to be worth the upgrade. The size of the Nex-6 is absolutely perfect for me, so I’ll be sticking with it for a while. If you want one, they’re available reasonably priced second hand at sub £400.

It’s been instrumental for a lot of my work – I digitized an entire tracksite on the side of a mountain in the Swiss Alps with the 55-210mm lens, and I’ve digitized small dinosaur tracks with the 16-50mm and 35 mm lenses.

High Speed Camera

For most of the videos on my Animals in Motion youtube channel, and for collecting locomotion data during research, I’ve been using a high-speed camera from the slowmotion camera company. Unfortunately the model I purchased, for ~£1300 is no longer available. The closest now on the website is the fps4000 Lite, which costs £1900 + tax and shipping, which has considerably more memory and performance than the model I got. It’s not exactly pocket money (especially given modern phones, as outlined below), but it’s affordable compared to bigger high-speed cameras from the more mainstream companies like Photron.

The camera itself is rough and ready – it doesn’t have what the tech world would call a ‘premium feeling’, and the interface both on the camera and on the desktop software is… finicky. I also had a few issues with actually getting the camera delivered after payment was made, as has a colleague at a different university, presumably because these things are being more or less made to order. Getting good videos out means downloading a thousand raw files per second of footage, then batch-processing them in something like photoshop, which can take a while especially on older hardware.

That being said, the results are absolutely fantastic:

The cameras can be linked up and synchronized if you want to use more than one.

Phone camera

They say that the best camera is the one you have on you when you need it. Given the quality of modern phone cameras, that’s never been truer. I’ve been using a Galaxy Note 8 for a few months now. I think it’s a tad overkill for my purposes, and I’ll probably go for something a bit cheaper next time (especially now that mid-range phones like Samsung’s new A9 still have fantastic camera set-ups).

For still images, it takes photos good enough for publications (though I’m yet to use a Phone’s picture in a paper), but it also takes slow motion video – 240 fps for quite a while, or 960 fps for a maximum of 1 second:

Shrimp swimming, recorded at 240fps with a Note 8:

Video of a Seagull taking off, recorded with a Galaxy Note 8 at 960 fps:

Light boxes

I previously discussed my photogrammetry set-up here. The short version is I use two sizes of light box, one for small objects (Amazon link), and one for much larger objects (Amazon link).

To be honest, the larger of the two comes in far less useful, and the lights it came with are not great, so I tend to shoot larger objects outside of the box and deal with the background in the photogrammetry software.

Dissection equipment:

I do occasionally do dissections as part of both teaching and research. A couple of Christmases ago, my wife bought me a nice set of dissection tools from Fine Science Tools (she also has a set from them). They’re nice tools, and feel like they’ll last me my career, which hopefully will be long and fruitful!